Variant report

Variant	rs7590030
Chromosome Location	chr2:128055967-128055968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:128048865..128053582-chr2:128054524..128059062,6	K562	blood:
2	chr2:128049457..128053223-chr2:128055226..128061434,6	MCF-7	breast:
3	chr2:128048039..128052903-chr2:128053347..128057785,8	MCF-7	breast:
4	chr2:128048207..128054006-chr2:128054524..128060290,9	K562	blood:
5	chr2:128053684..128055296-chr2:128055704..128057822,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163161	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1011019	0.86[ASW][hapmap];0.81[CEU][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs10209483	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10496661	0.86[ASW][hapmap];0.81[CEU][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs10850	0.86[ASW][hapmap];0.81[CEU][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1158867	0.81[MEX][hapmap]
rs11679414	1.00[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11680877	0.86[EUR][1000 genomes]
rs11683986	0.93[MEX][hapmap]
rs11691088	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11692990	0.81[EUR][1000 genomes]
rs12105051	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1604817	0.91[CEU][hapmap]
rs2069894	1.00[JPT][hapmap]
rs2069898	0.86[CEU][hapmap];0.82[YRI][hapmap]
rs2069904	0.81[ASW][hapmap];0.86[CEU][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.96[YRI][hapmap]
rs2404534	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2896979	0.85[EUR][1000 genomes]
rs3732209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3817088	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3958415	0.86[EUR][1000 genomes]
rs4150402	0.86[ASW][hapmap];0.81[CEU][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4150404	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150406	0.89[ASN][1000 genomes]
rs4150421	0.83[EUR][1000 genomes]
rs4150436	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4150452	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4150466	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4150471	0.81[CEU][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs4150474	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4150476	0.83[EUR][1000 genomes]
rs4150499	0.86[ASW][hapmap];0.80[CEU][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs4150519	0.89[ASN][1000 genomes]
rs4536600	0.87[CEU][hapmap];0.93[MEX][hapmap]
rs4662716	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4662718	0.81[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs4662719	0.82[EUR][1000 genomes]
rs4662720	0.86[ASW][hapmap];0.81[CEU][hapmap];0.80[LWK][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs58965651	0.89[ASN][1000 genomes]
rs5937	0.93[MEX][hapmap]
rs61422716	0.86[EUR][1000 genomes]
rs6753288	0.81[MEX][hapmap]
rs6755028	0.81[MEX][hapmap]
rs6757492	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72845975	0.86[EUR][1000 genomes]
rs72845976	0.86[EUR][1000 genomes]
rs72845979	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72845982	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72845991	0.82[EUR][1000 genomes]
rs72845993	0.82[EUR][1000 genomes]
rs72845997	0.82[EUR][1000 genomes]
rs72846002	0.83[EUR][1000 genomes]
rs7556675	0.86[ASW][hapmap];0.81[CEU][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes]
rs7599210	0.81[MEX][hapmap]
rs7607907	0.81[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs8179521	1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7590030	ERCC3	cis	parietal	SCAN
rs7590030	BIN1	cis	parietal	SCAN
rs7590030	ERCC3	cis	Esophagus Muscularis	GTEx
rs7590030	ERCC3	cis	cerebellum	SCAN
rs7590030	ERCC3	cis	Nerve Tibial	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128052000-128066200	Weak transcription	Spleen	Spleen
2	chr2:128052200-128062600	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:128052200-128062600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:128052200-128062600	Weak transcription	Thymus	Thymus
5	chr2:128052200-128062800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:128052200-128063200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:128052200-128063600	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:128052200-128063600	Weak transcription	Left Ventricle	heart
9	chr2:128052200-128063600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:128052200-128063800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:128052200-128065000	Weak transcription	Aorta	Aorta
12	chr2:128052200-128065000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:128052200-128066000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:128052200-128066200	Weak transcription	Small Intestine	intestine
15	chr2:128052400-128058600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:128052400-128058600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:128052400-128059800	Weak transcription	Fetal Lung	lung
18	chr2:128052400-128061800	Weak transcription	Brain Anterior Caudate	brain
19	chr2:128052400-128062000	Weak transcription	Primary T cells from cord blood	blood
20	chr2:128052400-128062600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:128052400-128062600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:128052400-128062800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:128052400-128062800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:128052400-128063000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:128052400-128063200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:128052400-128063400	Weak transcription	Psoas Muscle	Psoas
27	chr2:128052400-128063600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:128052400-128063600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:128052400-128063600	Weak transcription	Fetal Brain Female	brain
30	chr2:128052400-128063600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:128052400-128063800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:128052400-128063800	Weak transcription	Brain Substantia Nigra	brain
33	chr2:128052400-128064800	Weak transcription	NH-A	brain
34	chr2:128052400-128065000	Weak transcription	Fetal Stomach	stomach
35	chr2:128052400-128070400	Weak transcription	Esophagus	oesophagus
36	chr2:128052400-128070800	Weak transcription	Colonic Mucosa	Colon
37	chr2:128052400-128071200	Weak transcription	Fetal Brain Male	brain
38	chr2:128052600-128061600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:128052600-128062000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:128052600-128062000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:128052600-128062000	Weak transcription	Fetal Intestine Large	intestine
42	chr2:128052600-128062600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:128052600-128062600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:128052600-128062600	Weak transcription	Fetal Thymus	thymus
45	chr2:128052600-128062800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:128052600-128063000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:128052600-128063000	Weak transcription	Adipose Nuclei	Adipose
48	chr2:128052600-128063400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:128052600-128063600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:128052600-128063600	Weak transcription	HSMM	muscle

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